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Literature DB >> 12519946

CORG: a database for COmparative Regulatory Genomics.

C Dieterich¹, H Wang, K Rateitschak, H Luz, M Vingron.

Abstract

Sequence conservation in non-coding, upstream regions of orthologous genes from man and mouse is likely to reflect common regulatory DNA sites. Motivated by this assumption we have delineated a catalogue of conserved non-coding sequence blocks and provide the CORG-'COmparative Regulatory Genomics'-database. The data were computed based on statistically significant local suboptimal alignments of 15 kb regions upstream of the translation start sites of, currently, 10 793 pairs of orthologous genes. The resulting conserved non-coding blocks were annotated with EST matches for easier detection of non-coding mRNA and with hits to known transcription factor binding sites. CORG data are accessible from the ENSEMBL web site via a DAS service as well as a specially developed web service (http://corg.molgen.mpg.de) for query and interactive visualization of the conserved blocks and their annotation.

Entities: Species

Mesh：

Year: 2003 PMID： 12519946 PMCID： PMC165454 DOI： 10.1093/nar/gkg007

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

12 in total

1. The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data.

Authors: Viviane Praz; Rouaïda Périer; Claude Bonnard; Philipp Bucher
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

2. The Ensembl genome database project.

Authors: T Hubbard; D Barker; E Birney; G Cameron; Y Chen; L Clark; T Cox; J Cuff; V Curwen; T Down; R Durbin; E Eyras; J Gilbert; M Hammond; L Huminiecki; A Kasprzyk; H Lehvaslaiho; P Lijnzaad; C Melsopp; E Mongin; R Pettett; M Pocock; S Potter; A Rust; E Schmidt; S Searle; G Slater; J Smith; W Spooner; A Stabenau; J Stalker; E Stupka; A Ureta-Vidal; I Vastrik; M Clamp
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

CORG: a database for COmparative Regulatory Genomics.

1. The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data.

2. The Ensembl genome database project.

3. Transcriptional regulation of the stem cell leukemia gene (SCL)--comparative analysis of five vertebrate SCL loci.

4. rVista for comparative sequence-based discovery of functional transcription factor binding sites.

5. Conserved noncoding sequences are reliable guides to regulatory elements.

6. Exon discovery by genomic sequence alignment.

7. GeneNest: automated generation and visualization of gene indices.

8. A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons.

9. Annotating regulatory DNA based on man-mouse genomic comparison.

10. The distributed annotation system.

1. Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat.

2. Fast and reliable prediction of noncoding RNAs.

3. Context specific transcription factor prediction.

4. Recent computational approaches to understand gene regulation: mining gene regulation in silico.

5. The focal adhesion scaffolding protein HEF1 regulates activation of the Aurora-A and Nek2 kinases at the centrosome.

6. Toucan: deciphering the cis-regulatory logic of coregulated genes.

7. Ab initio identification of putative human transcription factor binding sites by comparative genomics.

8. Transient activation of meox1 is an early component of the gene regulatory network downstream of hoxa2.

9. Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals.

10. smyRNA: a novel Ab initio ncRNA gene finder.